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Genomic Scaffold Filling: A Progress Report

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Frontiers in Algorithmics (FAW 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9711))

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Abstract

The genomic scaffold filling problem has attracted a lot of attention since 2010. The general problem is on filling an incomplete sequence (sequence scaffold) I into \(I'\), with respect to a complete reference genome G, such that the number of adjacencies between G and \(I'\) is maximized. The problem is NP-complete and APX-hard, and admits a 1.2-approximation. In this survey paper, we will first review the progress being made for this setting.

However, the sequence input I is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). Then, we will review the most recent progress on this new version of the genomic scaffold filling problem where, (1) a scaffold S is given, the missing genes \(X=c(G)-c(S)\) can only be inserted in between the contigs, and the objective is to maximize the number of adjacencies between G and the filled \(S'\), and (2) a scaffold S is given, a subset of the missing genes \(X'\subset X=c(G)-c(S)\) can only be inserted in between the contigs, and the objective is still to maximize the number of adjacencies between G and the filled \(S''\). Some open problems will be posed for further research.

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Acknowledgments

I would like to thank my collaborators for this series of research: Chenglin Fan, Haitao Jiang, Nan Liu, David Sankoff, Boting Yang, Chunfang Zheng, Farong Zhong, Daming Zhu and Peng Zou.

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Authors and Affiliations

  1. Department of Computer Science, Montana State University, Bozeman, MT, 59717-3880, USA

    Binhai Zhu

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  1. Binhai Zhu
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Correspondence to Binhai Zhu .

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Editors and Affiliations

  1. Shandong University, Jinan, China

    Daming Zhu

  2. MS EC-31, University of Texas at Dallas, Richardson, Texas, USA

    Sergey Bereg

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Zhu, B. (2016). Genomic Scaffold Filling: A Progress Report. In: Zhu, D., Bereg, S. (eds) Frontiers in Algorithmics. FAW 2016. Lecture Notes in Computer Science(), vol 9711. Springer, Cham. https://doi.org/10.1007/978-3-319-39817-4_2

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  • DOI: https://doi.org/10.1007/978-3-319-39817-4_2

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-39816-7

  • Online ISBN: 978-3-319-39817-4

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